2006 Honda Civic Sedan with flashing green key light on dashboard

Sounds like a dead button cell battery in your key to me. Do you have a second key you can try?

EDIT: In my Mazda I get the flashing green key symbol with a dead key fob battery when trying to use the keyless starting feature and have to start the car with the actual key. I thought the OP may have had the same kind of system. According to @narkeleptk Honda's use the green key to represent a problem with the immobilizer, so my answer is not relevant to this question

There are a few possibilities that cause intermittent issues with the immobilizer. Here are a few I run into with 1 being the most common.

1. The key gets damaged. If its the remote head key then this year/model uses an integrated circuit for keyless entry and transponder. Its very common that the antenna for the transponder gets broken/loose solder joints. Its also common they suffer water damage and the circuit fails completely. Both of these can causes intermittent failures of the code being transmitted.

2. Low car battery. The immobilizer system on Honda's do not like to work with low voltage. ( If the locksmith tried making a new key then I would probably lean to this one being your problem or #3.)

3. The immobilizer/key antenna around the ignition starts to fail.

4. Water damage in MUX. (interior fuse box)

5. Wiring/grounding issue's in any one of the modules that are part of the immobilizer chain. (IMMO,MUX,ECU)

Something you can try is to bridge pins 4 & 5 of the OBD2 port with a paper clip. There is a known grounding issue with some of these cars that this is a temporary fix for. I don't know the full gyst of it but if bridging the pins work then its easy to google the full fix for it. I have had to bridge a few for my repo clients. Maybe the mechanic removed the a previous bridge to hook in their scan tool. It causes similar issue's with the immobilizer along with a slew of other oddities.